This R script is used to replace specified multiple amino acids to a selected amino acid. It is useful for exploratory analysis and selecting potential proteins to be used in future experiments.
Initial purpose of this script was to select a target protein to be used as a template for a Poly-Phe protein in 2016 Vilnius iGEM project.
To use this R script, you need:
- R ("data.table", "foreach", "ggplot2" packages)
- FoldX
- rotabase.txt (comes with FoldX)
- target.pdb file
All of these need to be in the same folder
Simply type Rscript --vanilla FoldX_template.R target.pdb number_of_runs omits.txt. The number of runs is an integer and omits.txt is an optional
file containing a list of positions to ignore.
Used with output .csv file from FoldX_template.R. The usage is as follows
Rscript --vanilla mutateDNA.R arg1 arg2 arg3 arg4, where:
arg1 - .fasta file containing original DNA sequence
arg2 - mutation_file.csv from FoldX_template.R
arg3 - number of mutations to perform
arg4 - codon to change into (ttc for PHE)
The script creates a folder called out_[PDB_name] which includes:
- A list of performed mutations with free energy change (cumulative).
- A plot showing energy change after each mutation compared to wild-type.
- Another plot showing local minimums.
- A folder containing FASTA files for each of these minimums.
Some pdb files simply do not work because of flaws in FoldX itself. Currently, only the first chain of target protein will be mutated. The target protein sequence must start at position 1.